I read an interesting fanfiction a while back, that talked about the capture of pokemon. They had a very nice explanation:
"When a Pokeball captures a Pokemon, it emits a ray of particles that disrupt the atoms in the target's body. This causes them to break down, converting a great deal of a Pokemon's mass into pure energy. This is what allows Pokemon to be stored in a Pokeball, which is much smaller than its body.The energy produced in this way is drawn up into the Pokeball through the use of energy-absorbing metals in its interior. Additional products of this reaction, mainly stray particles, or radiation, are also collected and drawn into the ball's interior. This allows the conversion process of a fission reaction without all of the mess and inconvenience of a nuclear explosion. A containment field within the Pokeball is then activated, which prevents the escape of the particles and energy generated by the capture process.
At this point, the Pokemon struggles to break free of the Pokeball. You see, this is where the second important difference comes into play; Pokemon retain their conscious soul even when deprived of many of the things that constitute a physical "body." We are perhaps more closely linked to the energy that courses through us than to any physical vessel. We therefore are consciously able to fight the capture process. A Pokemon will struggle against the containment field within the Pokeball; if its constraints can be broken, then we have the power to return our atoms to their original state.
The Pokeball captures and contains all energy and by-products of the reaction, yes? The reaction produced the energy, and by expending it again, it is possible to force the atoms back together and re-form the Pokemon's physical body. If the containment field is breached, the Pokeball will automatically open to allow the Pokemon to escape rather than be crushed in the tiny space.
The containment field cannot sustain itself, being powered by a battery implanted in the Pokeball upon its manufacture. It merely prevents the Pokemon from escaping while a second process takes place. A small amount of energy created during the reaction is siphoned off and stored in a special mechanism in the Pokeball's interior. With that energy goes a small piece of the Pokemon's soul. When this task is accomplished, the Pokemon has run out of time to escape. The Pokeball expels all air from its interior, creating a vacuum, and the containment field dissipates. This is the click or clunk that you hear when your Pokeball ceases to shake and the locks shut. Essentially, it has downloaded a small part of the Pokemon's being and stored it within its circuitry."
I found it a sad, but alse a very nice explantation how the pokeballs seals a part of a Pokemon's souls. It also adds that if somehow body and soul get seperated, the soul turns into some sort of Will-o'Whisp, and the body becomes a mindless doll. Gave me the creeps.
Story can be found here.